MolNFT v1 · #102176 · protein
4E10 germline encoded precursor NO.7 in complex with epitope scaffold T117
4ODX · 4E10 epitope scaffold T117: “4E10 germline encoded precursor NO.7 in complex with epitope scaffold T117”. X-ray diffraction, 6 pockets (best druggability 0.69). MolNFT v1 #102176 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4ODX
- Type
- protein
- Length
- 775 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4E10 epitope scaffold T117; GEP7 fv heavy chain; GEP7 fv light chain
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X | 4E10 epitope scaffold T117 | protein | 152 | 44% helix, 24% strand | — |
| A, H | GEP7 fv heavy chain | protein | 127 | 2% helix, 52% strand | — |
| B | GEP7 fv light chain | protein | 107 | 6% helix, 52% strand | — |
| L | GEP7 fv light chain | protein | 109 | 6% helix, 53% strand | — |
| Y | 4E10 epitope scaffold T117 | protein | 153 | 44% helix, 24% strand | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.69 | 0.76 | 74 | empty |
| 2 | 107 | 0.57 | 0.85 | 20 | empty |
| 3 | 115 | 0.42 | 0.77 | 21 | empty |
| 4 | 93 | 0.40 | 0.77 | 19 | empty |
| 5 | 65 | 0.30 | 0.74 | 17 | empty |
Interfaces
8 interfaces between chains.
- B–H · 762 Ų buried · 7 hydrogen bonds · protein-protein
- A–L · 754 Ų buried · 6 hydrogen bonds · protein-protein
- A–Y · 734 Ų buried · 5 hydrogen bonds · protein-protein
- X–H · 721 Ų buried · 4 hydrogen bonds · protein-protein
- X–B · 224 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4ODX · 4E10 germline encoded precursor no.7 in complex with epitope scaffold T117 · the same entry in another collection · chain X against X, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 4ODX · PDBe 4ODX
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